RetrogeneDB ID: retro_shar_378

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841549.1:751089..751605(+)
• Located in intron of: ENSSHAG00000008514

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CETN1
• Ensembl ID: ENSSHAG00000015319
• Aliases: None
• Description: centrin, EF-hand protein, 1 [Source:HGNC Symbol;Acc:1866]

Sequence

>retro_shar_378
GCCAGCGCCTTGAAGAAGCCAAACCTGGGCTCTGCTGCCCCGCCAAGAAAGAAGCTGGGCCCCAAACCCGAGCTCGCAGA
GGAGCAGAAGCAGGAAATTAGAGAGGCGTTTGATCTCTTTGATACCGATGGAACGGGGACGGTGGATGTTAAGGAGCTCA
AGGTGGCTTTGAGAGCTCTGGGCTTTGAACCCAAGAAAGAAGAGATCAAAAAAATCATAACAGACACTGACAAGGAGGGG
ACGGGGAAAATCAGTTTCAATGACTTCTTGGCTGTGATGACGCAAAAAATGGCAGAAAAGGATACCAAAGAAGACATTCT
GAAGGCATTCAGACTCTTCGATGATGATGAAACTGGAAAAATCTCTTTCAAGAACTTAAAACGGGTGGCGAGAGAGCTAG
GGGAGAACCTCACCGATGAGGAACTACAAGAAATGATTGACGAAGCTGATCGGGATGGTGATGGAGAGGTCAACGAACAA
GAGTTCCTGCGGATCATGAAAAAGAACAATCTGTAT

Alignment

ORF - retro_shar_378 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 92.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASTIKKPNLGSA-PPRKKMGPKPELTEEQKQEIREAFDLFDTDGTGTIDVKELKVAMRALGFEPKKEEIK
          AS..KKPNLGSA.PPRKK.GPKPEL.EEQKQEIREAFDLFDTDGTGT.DVKELKVA.RALGFEPKKEEIK
Retrocopy ASALKKPNLGSAAPPRKKLGPKPELAEEQKQEIREAFDLFDTDGTGTVDVKELKVALRALGFEPKKEEIK

Parental  KMISDIDKEGTGKISFNDFLAVMTQKMAEKDTREEILKAFRLFDDDETGKISFKNLKRVARELGENLTDE
          K.I.D.DKEGTGKISFNDFLAVMTQKMAEKDT.E.ILKAFRLFDDDETGKISFKNLKRVARELGENLTDE
Retrocopy KIITDTDKEGTGKISFNDFLAVMTQKMAEKDTKEDILKAFRLFDDDETGKISFKNLKRVARELGENLTDE

Parental  ELQEMIDEADRDGDGEVNEQEFLRIMKKTSLY
          ELQEMIDEADRDGDGEVNEQEFLRIMKK..LY
Retrocopy ELQEMIDEADRDGDGEVNEQEFLRIMKKNNLY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_378 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013823	2 retrocopies	retro_meug_1093, retro_meug_856,
Monodelphis domestica	ENSMODG00000005932	1 retrocopy	retro_mdom_87,
Sarcophilus harrisii	ENSSHAG00000015319	2 retrocopies	retro_shar_237, retro_shar_378 ,